Initial Data Exploration

SomaLogic Data QC

Aptamer Descriptions

Table 1: List of aptamers grouped by organism and type categories, with number of aptamers per category shown in right-most column.

Organism Type Aptamer_Count
Human Protein 7289
Mouse Protein 233
Human Spuriomer 20
Human Hybridization Control Elution 12
Human Non-Biotin 10
Human Non-Cleavable 4
African clawed frog Non-Human 3
Gila monster Non-Human 3
Hornet Non-Human 3
Jellyfish Non-Human 3
Mouse Non-Human 3
Thermus thermophilus Non-Human 3
Common eastern firefly Non-Human 2
European elder Non-Human 2
Bacillus stearothermophilus Non-Human 1
Ensifer meliloti Non-Human 1
HIV-1 Protein 1
HIV-2 Protein 1
Red alga|Red alga Non-Human 1
strain K12 Non-Human 1

Table 2: Number of human protein aptamers (7289, see Table 1) per quality category. Quality refers to the success with which the human protein-designed aptamer is able to quantify protein intensity in mouse plasma samples.

Quality Count
High 2653
Low 910
Medium 3726

Proteomic Depth of Coverage

Figure 1: Plots of aptamer counts per sample for A) mouse and B) human datasets above eLoD calculated for each aptamer (eLoD = Median_blank + 4.9MAD_blank). Blue horizontal line indicate the total number of aptamers in the panel (7596). Red horizontal line (mouse only) indicates the number of human protein aptamers assessed to perform with high/medium quality in mouse samples.

Figure 2: Plots of aptamer counts per sample for A) mouse and B) human pre-normalization datasets above eLoD calculated for each aptamer (eLoD = Median_blank + 4.9MAD_blank). Blue horizontal line indicate the total number of aptamers in the panel (7596). Red horizontal line (mouse only) indicates the number of human protein aptamers assessed to perform with high/medium quality in mouse samples.

Assess Assay Variablity

Figure 3: Boxplots showing distribution of aptamer intensities by sample for mouse and human datasets, final data and pre-normalization data for each. Plots are color coded by clinical group for both datasets. Most samples in each dataset have similar intensity distributions. Calibrator samples and hemolysis samples (mouse only) show slightly wider distribution ranges. The sole AK mouse sample has a slightly lower-shifted distribution compared to other samples.

Figure X: Bar graph showing number of aptamers removed by eLoD filter per sample for mouse datasets.

Figure X: Boxplots showing distribution of removed aptamer counts per sample, grouped by aptamer quality in mouse. Outliers - samples with an irregular number of aptamers removed - are labeled.

Figure X: Bar graph showing number of aptamers removed by eLoD filter per sample for human datasets.

Figure X: Bar graph showing distribution of aptamers removed using eLoD filter, categorized by aptamer quality score in mouse system.

Figure X: Scatter plot showing the intensity distribution for three aptamers: seq.10000.28 (high quality aptamer in mouse), seq.10044.12 (low quality), and seq.10003.15 (medium quality). The low quality aptamer has higher variation then both the medium and high quality aptamers in both the normalized and pre-normalization mouse datasets, although the difference is more apparent in the normalized dataset.

SomaLogic Data Analysis

Mouse (Project Disney) Analysis

Assess Limit of Detection (Dilution Series) - PRE-NORMALIZATION DATA ONLY

Figure 4: P-value distributions for the wilcox tests performed on the mouse dilution series data (pre-normalization).

Figure 5: Volcano plots showing significantly differentially expressed proteins between mouse dilution series samples A) 35uL vs. 55uL, B) 35uL vs. 55uL Diluted [35uL sample, 20uL PBS], C) 55uL vs. 55uL Diluted.

Table X: Number of aptamers/proteins detected per mouse dilution series sample (pre-normalization). The 55uL Diluted samples have the lowest counts, but all are decently high (max 7596 aptamers).

Category Sample_ID AptCount
35uL Mouse 35 uL Rep 1 7512
35uL Mouse 35 uL Rep 2 7534
35uL Mouse 35 uL Rep 3 7540
55uL Mouse A Series Rep 1 7537
55uL Mouse A Series Rep 2 7537
55uL Mouse A Series Rep 3 7550
55uL Diluted Mouse B Series Rep 1 7491
55uL Diluted Mouse B Series Rep 2 7403
55uL Diluted Mouse B Series Rep 3 7421

Hemolysis Comparison

Figure X: P-value distributions for the Wilcox tests performed on the mouse data comparing intensity (RFU) values between aptamers in the Hemolysis and Pooled 55uL groups. A) Normalized mouse data, B) Pre-normalization mouse data.

Figure X: Volcano plots showing significantly differentially expressed proteins between hemolysis and pooled 55uL groups in mouse data, A) normalized, B) pre-normalization.

Table_Key Aptamer_Target Target_Full_Name
1 seq.17137.160_Beta-globin Hemoglobin subunit beta
2 seq.18198.51_HBAT Hemoglobin subunit theta-1
3 seq.19774.8_HBG2 Hemoglobin subunit gamma-2
4 seq.4915.64_Hemoglobin Hemoglobin
5 seq.6919.3_HBAZ Hemoglobin subunit zeta
6 seq.6992.67_HBD Hemoglobin subunit delta
7 seq.7136.107_Hemoglobin epsilon chain Hemoglobin subunit epsilon
8 seq.7965.25_HBAT Hemoglobin subunit theta-1
9 seq.9025.5_AHSP Alpha-hemoglobin-stabilizing protein

Table_Key Aptamer_Target Target_Full_Name
1 seq.3054.3_Haptoglobin, Mixed Type Haptoglobin
2 seq.7905.30_HPT Haptoglobin isoform 2

KMC-PDAC v. KP Late:

Reveals differentially abundant proteins in autochthonous PDAC model

Figure X: P-value distributions for the wilcox tests performed on the mouse data comparing intensity (RFU) values between aptamers in the KMC-PDAC and Healthy Control - Late/KP Late groups. A) Normalized mouse data, B) Pre-normalization mouse data.

Figure X: Volcano plots showing significantly differentially expressed proteins between KMC - PDAC and Healthy Control - Late/KP Late groups in mouse data, A) normalized, B) pre-normalization.

KPC-Lung v. KP Late:

Reveals differentially abundant proteins in autochthonous lung cancer model

Figure X: P-value distributions for the Wilcox tests performed on the mouse data comparing intensity (RFU) values between proteins in the KPC-Lung and KP Late groups. A) Normalized mouse data, B) Pre-normalization mouse data.

Figure X: Volcano plots showing significantly differentially expressed proteins between KPC-Lung and Healthy Control - Late/KP Late groups in mouse data, A) normalized, B) pre-normalization.

KMC v. KMC-Control:

Reveals differentially abundant proteins in autochthonous Myc-driven PDAC model

Figure X: P-value distributions for the Wilcox tests performed on the mouse data comparing intensity (RFU) values between proteins in the KMC-PDAC and KMC Control groups. A) Normalized mouse data, B) Pre-normalization mouse data.

Figure X: Volcano plots showing significantly differentially expressed proteins between KMC-PDAC and KMC Control groups in mouse data, A) normalized, B) pre-normalization.

Figure X: P-value distributions for the t-tests performed on the mouse data comparing intensity (RFU) values between proteins in the KMC-PDAC and KMC Control groups. A) Normalized mouse data, B) Pre-normalization mouse data.

Figure X: Volcano plots of t-test results showing significantly differentially expressed proteins between KMC-PDAC and KMC Control groups in mouse data, A) normalized, B) pre-normalization.

KPC-Early v. KP Early:

Reveals differentially abundant proteins in early lethal PanIN model

Figure X: P-value distributions for the Wilcox tests performed on the mouse data comparing intensity (RFU) values between proteins in the KPC - Early and Healthy control - early/KP-early groups. A) Normalized mouse data, B) Pre-normalization mouse data.

Figure X: Volcano plots showing significantly differentially expressed proteins between KPC - early and Healthy control - early/KP - early groups in mouse data, A) normalized, B) pre-normalization.

KPC-Late (Lethal PanIN – Late) v. KP Late:

Reveals differentially abundant proteins in late lethal PanIN model

Figure X: P-value distributions for the Wilcox tests performed on the mouse data comparing intensity (RFU) values between proteins in the Lethal PanIN - Late/KPC - Late and Healthy Control - Late/KP-Late groups. A) Normalized mouse data, B) Pre-normalization mouse data.

Figure X: Volcano plots showing significantly differentially expressed proteins between Lethal PanIN - Late/KPC - Late and Healthy Control - Late/KP-Late groups in mouse data, A) normalized, B) pre-normalization.

KC-Late v. KP Late:

Reveals differentially abundant proteins in non-lethal PanIN model

Figure X: P-value distributions for the Wilcox tests performed on the mouse data comparing intensity (RFU) values between proteins in the Non-lethal PanIN - Late/KC - Late and Healthy Control - Late/KP-Late groups. A) Normalized mouse data, B) Pre-normalization mouse data.

Figure X: Volcano plots showing significantly differentially expressed proteins between Non-lethal PanIN - Late/KC - Late and Healthy Control - Late/KP-Late groups in mouse data, A) normalized, B) pre-normalization.

Human (Project Orion) Analysis

Assess Limit of Detection (Dilution Series) - PRE-NORMALIZATION DATA ONLY

Figure 6: P-value distributions for the wilcox tests performed on the human dilution series data (pre-normalization).

Figure 7: Volcano plots showing significantly differentially expressed proteins between human dilution series samples A) 35uL vs. 55uL, B) 35uL vs. 55uL Diluted [35uL sample, 20uL PBS], C) 55uL vs. 55uL Diluted.

Table X: Number of aptamers/proteins detected per human dilution series sample (pre-normalization). The 55uL Diluted samples have the lowest counts, but all are decently high (max 7596 aptamers).

Category Sample_ID AptCount
35uL Human 35 uL Rep 1 7553
35uL Human 35 uL Rep 2 7558
35uL Human 35 uL Rep 3 7561
55uL Human A Series Rep 1 7566
55uL Human A Series Rep 2 7576
55uL Human A Series Rep 3 7577
55uL Diluted Human B Series Rep 1 7503
55uL Diluted Human B Series Rep 2 7482
55uL Diluted Human B Series Rep 3 7504

Case (Adenocarcinoma) v. All Controls

Figure X: P-value distributions for the Wilcox tests performed on the human data comparing intensity (RFU) values between proteins in the Case (Adenocarcinoma) and All Controls groups. A) Normalized human data, B) Pre-normalization human data.

Figure X: Volcano plots showing significantly differentially expressed proteins between Case (Adenocarcinoma) and All Controls groups in human data, A) normalized, B) pre-normalization.

Case (Adenocarcinoma) v. Control (Benign)

Figure X: P-value distributions for the Wilcox tests performed on the human data comparing intensity (RFU) values between proteins in the Case (Adenocarcinoma) and Control (Benign) groups. A) Normalized human data, B) Pre-normalization human data.

Figure X: Volcano plots showing significantly differentially expressed proteins between Case (Adenocarcinoma) and Control (Benign) groups in human data, A) normalized, B) pre-normalization.

Case (Adenocarcinoma) v. Control (Benign Prostatic Hyperplasia)

Figure X: P-value distributions for the Wilcox tests performed on the human data comparing intensity (RFU) values between proteins in the Case (Adenocarcinoma) and Control (Benign Prostatic Hyperplasia) groups. A) Normalized human data, B) Pre-normalization human data.

Figure X: Volcano plots showing significantly differentially expressed proteins between Case (Adenocarcinoma) and Control (Benign Prostatic Hyperplasia) groups in human data, A) normalized, B) pre-normalization.

Case (Adenocarcinoma) v. Control (Prostatic intraepithelial neoplasia)

Figure X: P-value distributions for the Wilcox tests performed on the human data comparing intensity (RFU) values between proteins in the Case (Adenocarcinoma) and Control (Prostatic Intraepithelial Neoplasia) groups. A) Normalized human data, B) Pre-normalization human data.

Figure X: Volcano plots showing significantly differentially expressed proteins between Case (Adenocarcinoma) and Control (Prostatic Intraepithelial Neoplasia) groups in human data, A) normalized, B) pre-normalization.

Somalogic vs. Seer Proteograph

Protein ID Overlap & Fold Change Comparison - KMC-PDAC v. KMC Control

Protein ID Overlap & Fold Change Comparison - Human Case v. All Control